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TAFA4 TAFA chemokine like family member 4 [ Homo sapiens (human) ]

Gene ID: 151647, updated on 2-Nov-2024

Summary

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Official Symbol
TAFA4provided by HGNC
Official Full Name
TAFA chemokine like family member 4provided by HGNC
Primary source
HGNC:HGNC:21591
See related
Ensembl:ENSG00000163377 MIM:617498; AllianceGenome:HGNC:21591
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TAFA-4; FAM19A4
Summary
This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that act as regulators of immune and nervous cells. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]
Expression
Biased expression in adrenal (RPKM 8.7), gall bladder (RPKM 0.7) and 1 other tissue See more
Orthologs
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Genomic context

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See TAFA4 in Genome Data Viewer
Location:
3p14.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (68731766..68932547, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (68769008..68969284, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (68780917..68981698, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:68693138-68693638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:68693639-68694139 Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 8 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:68859761-68860260 Neighboring gene RNA, 5S ribosomal pseudogene 135 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:68968097-68968699 Neighboring gene Sharpr-MPRA regulatory region 589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14515 Neighboring gene EGF domain specific O-linked N-acetylglucosamine transferase Neighboring gene EOGT divergent transcript Neighboring gene TATA element modulatory factor 1 Neighboring gene microRNA 3136

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Methylation analysis of the FAM19A4 gene in cervical scrapes is highly efficient in detecting cervical carcinomas and advanced CIN2/3 lesions. De Strooper LM, et al. Cancer Prev Res (Phila), 2014 Dec. PMID 25281488
  2. Comparing the performance of FAM19A4 methylation analysis, cytology and HPV16/18 genotyping for the detection of cervical (pre)cancer in high-risk HPV-positive women of a gynecologic outpatient population (COMETH study). Luttmer R, et al. Int J Cancer, 2016 Feb 15. PMID 26317579
  3. FAM19A4 methylation analysis in self-samples compared with cervical scrapes for detecting cervical (pre)cancer in HPV-positive women. Luttmer R, et al. Br J Cancer, 2016 Aug 23. PMID 27415009, Free PMC Article
  4. The clinical significance of FAM19A4 methylation in high-risk HPV-positive cervical samples for the detection of cervical (pre)cancer in Chinese women. Bu Q, et al. BMC Cancer, 2018 Nov 29. PMID 30486875, Free PMC Article
  5. [Detection and analysis of FAM19A4 promoter methylation in cervical exfoliated cells]. Wang SF, et al. Zhonghua Yi Xue Za Zhi, 2019 Jul 2. PMID 31269601

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Signals from the TAFA4-PTEN-PU.1 axis alleviate nasal allergy by modulating the expression of FcepsilonRI in mast cells.
    Title: Signals from the TAFA4-PTEN-PU.1 axis alleviate nasal allergy by modulating the expression of FcεRI in mast cells.
  2. FAM19A4/miR124-2 Methylation Testing and Human Papillomavirus (HPV) 16/18 Genotyping in HPV-Positive Women Under the Age of 30 Years.
    Title: FAM19A4/miR124-2 Methylation Testing and Human Papillomavirus (HPV) 16/18 Genotyping in HPV-Positive Women Under the Age of 30 Years.
  3. Full genotyping and FAM19A4/miR124-2 methylation analysis in high-risk human papillomavirus-positive samples from women over 30 years participating in cervical cancer screening in Orebro, Sweden.
    Title: Full genotyping and FAM19A4/miR124-2 methylation analysis in high-risk human papillomavirus-positive samples from women over 30 years participating in cervical cancer screening in Örebro, Sweden.
  4. Clinical Regression of High-Grade Cervical Intraepithelial Neoplasia Is Associated With Absence of FAM19A4/miR124-2 DNA Methylation (CONCERVE Study).
    Title: Clinical Regression of High-Grade Cervical Intraepithelial Neoplasia Is Associated With Absence of FAM19A4/miR124-2 DNA Methylation (CONCERVE Study).
  5. Risk-stratification of HPV-positive women with low-grade cytology by FAM19A4/miR124-2 methylation and HPV genotyping.
    Title: Risk-stratification of HPV-positive women with low-grade cytology by FAM19A4/miR124-2 methylation and HPV genotyping.
  6. Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.
    Title: Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.
  7. Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions.
    Title: Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions.
  8. FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.
    Title: FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.
  9. The use of molecular markers for cervical screening of women living with HIV in South Africa.
    Title: The use of molecular markers for cervical screening of women living with HIV in South Africa.
  10. Among HPV positive women aged >/=30 years, a negative FAM19A4/miR124-2 methylation test provides a similar safety in terms of long-term CIN3+ risk compared with a negative cytology test, while the CIN3+risk following a positive methylation test justifies immediate colposcopy referral.
    Title: Long-term CIN3+ risk of HPV positive women after triage with FAM19A4/miR124-2 methylation analysis.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25161

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables receptor ligand activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables receptor ligand activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in macrophage chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in macrophage chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phagocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of membrane potential IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of signaling receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in superoxide anion generation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
chemokine-like protein TAFA-4
Names
family with sequence similarity 19 (chemokine (C-C motif)-like), member A4
family with sequence similarity 19 member A4, C-C motif chemokine like
protein FAM19A4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001005527.3 → NP_001005527.1  chemokine-like protein TAFA-4 precursor

    See identical proteins and their annotated locations for NP_001005527.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC096922, BC031566, DA017279
    Consensus CDS
    CCDS2907.1
    UniProtKB/Swiss-Prot
    A8MVT2, Q96LR4
    Conserved Domains (1) summary
    pfam12020
    Location:50 → 138
    TAFA; TAFA family

  2. NM_182522.5 → NP_872328.1  chemokine-like protein TAFA-4 precursor

    See identical proteins and their annotated locations for NP_872328.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC096922, AY325117
    Consensus CDS
    CCDS2907.1
    UniProtKB/Swiss-Prot
    A8MVT2, Q96LR4
    Related
    ENSP00000295569.7, ENST00000295569.12
    Conserved Domains (1) summary
    pfam12020
    Location:50 → 138
    TAFA; TAFA family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    68731766..68932547 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533372.2 → XP_011531674.1  chemokine-like protein TAFA-4 isoform X1

    See identical proteins and their annotated locations for XP_011531674.1

    Conserved Domains (1) summary
    pfam12020
    Location:50 → 124
    TAFA; TAFA family

  2. XM_011533371.2 → XP_011531673.1  chemokine-like protein TAFA-4 isoform X1

    See identical proteins and their annotated locations for XP_011531673.1

    Conserved Domains (1) summary
    pfam12020
    Location:50 → 124
    TAFA; TAFA family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    68769008..68969284 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345323.1 → XP_054201298.1  chemokine-like protein TAFA-4 isoform X1

  2. XM_054345322.1 → XP_054201297.1  chemokine-like protein TAFA-4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96LR4.1 GenPept UniProtKB/Swiss-Prot:Q96LR4

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